Controlling the potential of primate neural stem cells by regulating pax6

ABSTRACT

A transcription factor both necessary and sufficient for human neuroectoderm specification, Pax6, as well as applications thereof, is disclosed.

CROSS-REFERENCE TO RELATED APPLICATION

This application claims priority from U.S. provisional patent application Ser. No. 61/273,373, filed on Aug. 3, 2009, and U.S. provisional patent application Ser. No. 61/273,690, filed on Aug. 6, 2009. Both of these applications are incorporated by reference herein.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under NS045926 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND

Somatic stem cells are undifferentiated cells that can renew themselves and can also differentiate to specialized cell types of a tissue or organ, such as neural stem cells and hematopoietic stem cells. While stem cells derived from an early embryo, known as embryonic stem cells (ESCs), can be maintained in culture for an extended period without losing their differentiation potential (Thomson et al., Science, 1998, 282:1145-1147; Evans & Kaufamn, Nature, 1981, 5819:154-156), somatic stem cells like brain (neural) or blood stem cells gradually lose their differentiation potentials when cultured for a long period of time. A brain stem cell can generate all types of cells in the brain and spinal cord but after expansion it can only generate neural cells of a particular brain region or even particular cell types of a brain region (Temple, Nat. Rev. Neurosci., 2001, 2:513-520; Gage, Science, 2000, 287:1433-1438).

Maintenance of ESCs depends on the transcription network orchestrated by stem cell (pluripotent) transcription factors including Oct4, Nanog, and Sox2. These transcription factors block developmental genes while activating stem cell genes, thus inhibiting differentiation and maintaining the stem cell state (Boyer et al., Cell, 2005, 122:947-956). Activation of this stem cell transcription network reprograms somatic (e.g. skin) cells to stem cells, also known as induced pluripotent stem cells (iPSCs) (Yu et al., Science, 2007, 318:1917-1920; Takahashi et al., Cell, 2007, 131:861-872).

Transplantation of hESC-differentiated neural derivatives often ends up with over-growth of the grafts (Roy et al., Nat. Med, 2006, 12: 1259-1268; Sonntag et al., Stem Cells, 2007, 25: 411-418). hESC derived neurons and glia are a desirable source of cells for replacement therapy. However, transplantation of stem cell derived neural cells for therapeutic purposes is often confounded by the tumorigenic potential of undifferentiated neuroepithelial cells.

Needed in the art is a method of maintaining primate somatic stem cells, such as brain stem cells, in culture without losing differentiation potential. Like the generation of iPSCs by pluripotent transcription factors, transcription factor(s) critical for maintaining neural stem cells would need to be identified and regulated. Also needed in the art is a method of decreasing the possibility of tumor formation in a transplant.

SUMMARY OF THE INVENTION

In one embodiment, the present invention is a primate primitive neural stem cell (primate pNSC) wherein the cell overexpresses Pax6.

In another embodiment, the present invention is a population of the primate pNSCs described above, wherein the cells overexpress Pax6. In a preferred embodiment, the cells continue to proliferate without differentiating, preferably for at least one week. Most preferably, the cells continue to proliferate without differentiating for at least two weeks. In a preferred embodiment, the cells are human pNSCs.

In yet another embodiment, the present invention is a method of creating a population of primate pNSCs from primate embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) comprising the step of overexpressing Pax6 within a population of ESCs or iPSCs, wherein the expression level of Pax6 is sufficient to suppress the expression of Sox1 and Oct4. In one embodiment, the primate is human.

In a preferred embodiment, the overexpression of Pax6 is via an inducible system. In another preferred embodiment, the overexpression of Pax6 is via a lentiviral vector, preferably an inducible lentiviral vector. In one preferred embodiment, the overexpression of Pax6 is under the control of elongation factor 1α promoter in the lentiviral vector. In yet another preferred embodiment, the overexpression of Pax6 is via adding recombinant Pax6 to the cells directly.

In yet another embodiment, the present invention is method of creating a population of primate regional neural stem cells comprising the steps of overexpressing Pax6 within a population of primate ESCs or iPSCs wherein the expression level of Pax6 is sufficient to suppress the expression of Sox1 and Oct4, and suppressing Pax6 expression and differentiating the cells into regional neural stem cells. Preferably, the regional neural stem cells are selected from the group consisting of forebrain cells, midbrain cells and spinal cells. Preferably, the primate is human.

In yet another embodiment, the present invention is a method of creating a population of primate pNSCs from primate regional neural stem cells comprising the step of overexpressing Pax6 within a population of primate regional neural stem or progenitor cells wherein the expression level of Pax6 is sufficient to reprogram the cells to the primate pNSC stage. Preferably, the primate is human.

In yet another embodiment, the present invention is a method of treating a patient with brain tumor or overgrowth of cell transplants by suppressing Pax6 expression comprising the steps of inhibiting Pax6 expression in the tumor cells or the overgrown cell transplants. Preferably, the suppression of Pax6 expression is through Pax6 RNAi, block of Pax6 transcription or acceleration of Pax6 degradation.

Other objects, advantages and features of the present invention will become apparent from the following specification taken in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF DRAWINGS

The invention will be better understood and features, aspects and advantages other than those set forth above will become apparent when consideration is given to the following detailed description thereof. Such detailed description makes reference to the following drawings, wherein:

FIG. 1A-D show expression of neural transcription factors in fetuses and along ESC differentiation. (FIG. 1A and FIG. 1B) Western blotting shows temporal expression of Pax6 and Sox1 along human and mouse ESC differentiation, respectively. Arrowheads, Pax6a (lower) and Pax6b (upper). (FIG. 1C) Pax6 and Sox2, but not Sox1, are expressed in pNSCs in the neural plate of day 18 and day 21 human fetuses and Sox1 is detected in regional NSCs of the brain and neural tube of day 26 human fetus. (FIG. 1D) Sox1 and Sox2 are expressed throughout the mouse neural plate (pNSCs) and neural tube (regional NSCs) from day 8 to 10.5 whereas Pax6 is absent in day 8 embryos but present in the forebrain and neural tube at day 10.5.

FIG. 2 demonstrates that hESCs and iPSCs use identical mechanisms for neural specification. H9 hESCs, H1 hESCs and human iPSCs are differentiated to pNSCs cells for 8 days, which are Pax6+/Sox1−. This demonstrated that hESCs and human iPSCs employ identical transcriptional networks for pNSCs specification and Pax6 represents an efficient way to convert human iPSCs to pNSCs, given their lower differentiation potential as compared to hESCs (Hu et al., Proc Natl Acad Sci USA, 2010, 107:4335-4340).

FIG. 3 shows expressions of Otx2, Pax6, Sox1 and FoxG1 in early monkey embryos. Similar to that of humans, rhesus monkey pNSCs are also Pax6+/Sox1− and Sox1 is only expressed in regional NSCs. This suggests that the transcriptional networks along pNSC specification are conserved within primates.

FIG. 4A-D demonstrates with transgenic hESC lines that Pax6 overexpression maintains cells in pNSC state. (FIG. 4A) hESC lines expressing inducible Pax6 isoforms. (FIG. 4B) GFP (control) is induced 48 h after Dox treatment. (FIG. 4C) Pax6-GFP is induced after 48 h of Dox treatment. Note Pax6-GPF in nuclei. (FIG. 4D) hESC lines expressing inducible Pax6 RNAi. (FIG. 4E) After differentiation to pNSCs at day 10, induction and maintenance of Pax6 by doxycycline treatment for 2 weeks kept growth factor-independent proliferation and suppressed Sox1 expression. 3 days after Dox removal, many cells began to express Sox1. These data indicate that maintaining of NSCs in a primitive state can be achieved by Pax6 overexpression and driving the cells out of the primitive state can also be achieved by shutting off Pax6 expression. In addition, the inducible transgenic overexpression/knockdown tool represents a useful strategy to control the cell fates.

FIG. 5A-B shows that downregulation of Pax6 in NSCs causes cell death and terminal differentiation. (FIG. 5A) hESCs were infected with lentiviruses bearing control (Luc) and Pax6b RNAi, and stable lines were established thereafter. Pax6b RNAi cells can not be maintained in a NSC state at day 17 as demonstrated by massive spontaneous differentiation. (FIG. 5B) Transiently infection of Pax6 RNAi lentiviruses targeting both Pax6a and Pax6b in day 14 NSCs caused massive cell death and neuronal differentiation.

FIG. 6A-B shows that overexpression of Pax6 reprograms regional NSCs to pNSCs. (FIG. 6A) Human cortical NSCs are infected with inducible lentiviruses expression of GFP control or Pax6. After withdrawal of Dox and five days of treatment with retinoid acid (RA), the GFP (control) expression regional NSCs stop growing whereas the Pax6-NSCs continue to grow with neurite extension. (FIG. 6B) Many of the Pax6-NSCs were positive for spinal cord marker, HoxB4, after treatment with RA but none of the GFP-NSCs express HoxB4. Since cortical NSCs are fixed to a cortical fate, the fact that Pax6 overexpression endows the cells with spinal cord differentiation potential indicates that the cells are reprogrammed to a primitive stage before RA mediated caudalization.

FIG. 7A-B shows that Pax6 expressing pNSCs within transplants are origins of tumor formation. (FIG. 7A) Pax6-expressing pNSCs were present in the dopamine neuron differentiation cultures (for 35 days) although the numbers gradually decrease over time. Midbrain TH positive neurons are lost in Parkinson's disease and TH neurons are specifically used for replacement therapy for Parkinson's disease. (FIG. 7B) One case of tumor formation after transplantation of the cells containing above mentioned pNSCs. These Pax6 positive cells are proliferating and are tumorigenic if they are transplanted to the brain of host mice. Arrow shows the tumor and the cells within the tumor are Pax6+/Sox1− pNSCs.

FIG. 8 demonstrates a non-genetic means to regulate Pax6 expression.

FIG. 9 shows the protein sequence of Pax6a (SEQ ID NO:112).

FIG. 10 shows the mRNA sequence of Pax6 transcription variant 1 (SEQ ID NO:113), which encodes Pax6a.

FIG. 11 shows the protein sequence of Pax6b (SEQ ID NO:114).

FIG. 12 shows the mRNA sequence of Pax6 transcription variant 2 (SEQ ID NO:115), which encodes Pax6b.l

FIG. 13 shows the mRNA sequence of Pax6 transcription variant 3 (SEQ ID NO:116), which encodes Pax6a.

FIG. 14 shows the protein sequence of Pax6aΔHD (SEQ ID NO:117), human Pax6a mutant with the homeodomain deleted.

FIG. 15 shows the mRNA sequence of Pax6aΔHD (SEQ ID NO:118).

FIG. 16 shows the protein sequence of Pax6ΔPAI (SEQ ID NO:119), human Pax6a mutant with the N-terminal Paired Domain deleted.

FIG. 17 shows the mRNA sequence of Pax6ΔPAI (SEQ ID NO:120).

FIG. 18 shows the protein sequence of Pax6ΔPD (SEQ ID NO:121), human Pax6a mutant with the entire Paired Domain deleted.

FIG. 19 shows the mRNA sequence of Pax6ΔPD (SEQ ID NO:122).

FIG. 20 shows the protein sequence of Pax6bD/N (SEQ ID NO:123), a Pax6b dominant negative mutant in which the PST transactivation domain is deleted.

FIG. 21 shows the mRNA sequence of Pax6bD/N (SEQ ID NO:124).

FIG. 22 is a scheme showing Pax6 in induction, maintenance, and reprogramming of primate pNSCs.

DESCRIPTION OF THE PRESENT INVENTION

The inventors have discovered that the transcription factor Pax6 is necessary and sufficient for induction of primate pNSCs, preferably human pNSCs, from ESCs (hESCs) and iPSCs, a role that does not apply to Pax6 in other non-primate animals (e.g. mice, Simpson and Price, Bioessays, 2002, 24:1041-1051). Additionally, Pax6 is important not just in induction but also in maintenance of stem cells in a primitive undifferentiated state.

Pax6 belongs to the paired box (Pax) gene family that plays a critical role in the development of several organ systems, including eye, pancreas and cerebrum (Chi et al., Trends Genet., 2002, 18:41-47). Pax6 is highly conserved, with 100% amino acid sequence homology between mouse and human, suggesting important functions across species. There are two main Pax6 isoforms created by alternative mRNA splicing of the fifth exon. Pax6b is produced by insertion of exon5a into the paired domain and is 14 amino acids longer than Pax6a with different DNA binding specificity (Epstein et al., Genes Dev., 1994, 8:2022-2034; Kozmik et al., EMBO J., 1997, 16:6793-6803).

The inventors have discovered that the way in which Pax6 acts is similar in function to the way Oct4 acts in ESCs. Pax6 represses stem cell genes, including Oct4 and Nanog, and induces neuroectoderm genes so that the ESCs convert to NSCs. At the same time, Pax6 blocks expression of genes involved in later-stage neural development, including Sox1, thus preventing NSCs from further differentiation. By doing so Pax6-expressing NSCs are in a primitive stage and capable of full-range neural differentiation, including the generation of projection neurons of the brain and spinal cord. During embryo development or expansion in culture, the primitive NSCs gradually down-regulate Pax6 and turn on late-stage neural genes, thus becoming committed neural progenitors that only generate particular types of neurons and glia.

The inventors discovered that the Pax6a isoform upregulates neural genes and directs the cells to primate pNSCs, although both Pax6a and Pax6b isoforms bind to the pluripotent gene promoters and down-regulate pluripotent genes.

FIG. 22 graphically describes the pathway that the inventors have discovered. This path is integral to the present invention. Overexpression of the Pax6 factor in primate pluripotent stem cells, such as hESCs and iPSCs, creates a population of undifferentiated dividing pNSCs. These pNSCs can be differentiated to neurons and supporting cells of the nervous system by decreasing Pax6 and under appropriate differentiation conditions.

FIG. 22 shows Pax6 in induction, maintenance, and reprogramming of primate pNSCs. In one embodiment, hESCs differentiate to regional NSCs via a transient intermediate stage, pNSCs, that express Pax6 at day 8-10. Pax6 induces hESC differentiation towards neural cells partly by inhibiting stem cell genes like Oct4 and keeps the NSCs in the primitive stage partly by inhibiting further differentiation to regional progenitors. Forced Pax6 expression reverses regional progenitors to pNSCs.

hESC derived neurons and glia are a desirable source of cells for replacement therapy. However, transplantation of stem cell derived neurons for therapeutic purposes is often confounded by the tumorigenic potential of undifferentiated neuroepithelial cells and thus ends up with over-growth of the grafts (Roy et al., Nat. Med, 2006, 12: 1259-1268; Sonntag et al., Stem Cells, 2007, 25: 411-418). These neuroepithelial cells or pNSCs are maintained in their state by the expression of Pax6. Thus, Pax6 downregulation in cultures prior to transplant will ensure that the pNSCs either differentiate or die, thus decreasing the possibility of tumor formation in the transplant.

Yet another embodiment of the invention recognizes that down-regulating Pax6 is also an efficient and safe way to control brain tumors which initiate from transformed pNSCs and show an increased expression of Pax6.

By “stem cell”, we mean to include all primate pluripotent stem cells. For example, we include both ESCs, such as hESC line H9, and iPSCs (Yu et al., Science, 2007, 318:1917-1920; Takahashi et al., Cell, 2007, 131:861-872).

By “primitive neural stem cell”, we mean Pax6⁺/Sox1⁻ cells that are characterized by early rosette morphology and have the full potential to differentiate into all types of neural cells in the body.

By “regional neural stem cell”, we mean Sox1⁺ neural progenitors with limited potential to differentiate into some but not all types of neural cells, including forebrain neural stem cells, midbrain neural stem cells and spinal neural stem cells. We mean to use the terms “progenitors” and “stem cells” interchangeably. For example, we mean to use the terms “regional neural progenitors” and “regional neural stem cells” interchangeably

In one embodiment, one can separate pNSCs from regional NSCs using the gene panel listed in Table 1 in Example 2. Expressions of these genes are down-regulated at least four folds in regional NSCs compared to pNSCs.

By “Pax6”, we mean the transcription factor paired box gene 6, preferably coordination of both isoforms of Pax6, including isoforms a and b of various species, preferably mammalian species. In one embodiment, one can use isoform a. The mRNA and protein sequences of the two isoforms of human Pax6 can be found at NCBI (NM_(—)000280, NM_(—)001127612, NM_(—)001604). The Pax6 gene is conserved among species (Quiring et al., Science, 1994; 265:785-789), but it is more conserved among mammals than it is in non-mammals. The Pax6 gene can be cloned from most mammalian cells expressing Pax6, such as human, rhesus monkey and mouse cells. We cloned Pax6a and Pax6b genes from the human NSCs differentiated from hESCs. Of course, one may make conservative or benign substitutions, deletions or additions to the native Pax6 sequences and we mean to include these substantially identical sequences in our definitions of “Pax6”. For example, one can use Pax6ΔHD (see SEQ ID NO:117 for the protein sequence) to direct the differentiation from stem cells to pNSCs.

Zhang et al. (Cell Stem Cell, 2010, 7:90-100) is an academic paper which describes one embodiment of the present invention and is incorporated herein by reference. Briefly, by genetic manipulation of ESCs, the inventors discovered that Pax6 is necessary and sufficient for neuroepithelial (NE) specification from human but not mouse ESCs. The inventors also found that cell lineage specification of ESCs not only requires repression of pluripotent genes but also depends on induction of the target lineage genes.

U.S. Pat. No. 7,588,937, US2008/0206865 and US2008/0227137 are patent or patent publications from the inventor's laboratory and disclose directed differentiation of neural cells. These references are also incorporated herein by reference.

Creation of a Population of Primate pNSC Cells

In one embodiment, the present invention is a population of primate pNSCs that overexpress Pax6. By “overexpression” of Pax6, we mean any expression over the amount of native Pax6 that is sufficient to convert stem cells to pNSCs. Overexpression of Pax6 will keep the cells in their primitive state, i.e. any Pax6 level that is sufficient to suppress the expression of Sox1 and Oct4. One can test for expression of Sox1 and Oct4 by methods of determining expression level of a gene through a number of methods, e.g. Western Blotting, immunostaining and polymerase chain reaction, which are well known in the art. Note that one can add exogenous Pax6 protein or recombinant Pax6 protein to the cells directly and keep the cells in the primitive state. This is also “overexpression”. By “exogenous” protein, we mean proteins produced outside the cell in question. For example, Pax6 protein might be purified and concentrated from human cells and added to the cell in question so that Pax6 is “overexpressed” in that cell. By “recombinant” protein, we mean a protein produced by genetic engineering.

One may wish to test that the cells remain in the primitive state. A preferable way to do that is to test for the suppressed expression of Sox 1 and Oct4, and the full neural range of differentiation potentials.

In one embodiment, the cells are created as follows: hESCs are incubated with Pax6 lentiviruses as described below, and grown on mouse embryonic fibroblast (MEF) feeder layer. Pax6-overexpressed cells gradually lose stem cell genes such as Oct4 and start to express neural genes except Sox1. Meanwhile, Pax6-expressing cells aggregate together to form early rosettes, a typical morphology of pNSCs. The population of pNSCs can be enriched through drug selection, such as blasticidin, G418 and puromycin, depending on which drug resistant gene is present in the lentiviral vector. One can also select for Pax6-positive pNSCs under a fluorescence microscope if a fluorescent protein is fused to Pax6, such as Pax6-GFP fusion protein.

In one embodiment, overexpression of Pax6 is driven by elongation factor (EF) 1α promoter. However, one can use other promoters as substitutes, for example, cytomegalovirus (CMV) promoter. More preferably, an inducible promoter is used and Pax6 is overexpressed using an inducible lentivirus system. Such inducible lentivirus systems are commercially available, for example, Lenti-X™ Tet-On® Advanced (Clontech, CA). In a preferred embodiment, Lenti-X™ Tet-On® Advanced is modified by replacing the CMV promoter driving rtTA-Advanced in the pLVX-Tet-On Advanced vector with the EF1α promoter. In this embodiment, expression of Pax6 is induced by doxycycline treatment, and removing doxycycline from the medium shuts off Pax6 expression from the vector.

In another embodiment, overexpression of Pax6 can also be achieved by viral infection, plasmid transfection or recombinant protein treatment of mutated Pax6.

In one embodiment, hESCs grown on MEF feeder layer are used for generating pNSCs. In another embodiment, ESCs are grown without MEF feeder layers. In yet another embodiment, iPSCs are used for generating pNSCs.

Expressing recombinant protein using lentiviral vector is well known in the art. Briefly, lentiviral transfer vector, lentiviral packaging plasmid and vesicular stomatitis virus G protein (VSV-G) would be cotransfected to packaging cells. Preferably, the packaging cells are HEK 293FT cells. 1-3 days after transfection, cell culture medium containing the viral particles is collected and filtered through a 0.45 μm filter to remove cell debris. Preferably, the viral particles are further concentrated by ultracentrifugation.

Other packaging cell lines are also available as substitutes for HEK 293FT cells. For example, NIH/3T3 cells can also be used for virus packaging.

Other types of viruses, for example, adenoviruses and retroviruses, can be used as substitutes. Expression modulation of Pax6 can also be achieved through transfection with plasmids, adding recombinant Pax6 in the medium, activating endogenous Pax6 expression through signaling molecules or small molecule drugs. Methods of plasmid transfection, purifying recombinant protein and small molecule screening are well known in the art.

In another embodiment, a population of primate pNSCs is created by exposing primate ESCs or iPSCs to an effective amount of Pax6 protein such that a population of primate pNSCs is created. Preferably, recombinant Pax6 can be purified and added into the medium in which the cells are cultured. Methods of purifying recombinant protein are well known in the art. Preferably, cells within the population continue to proliferate without differentiating and have the full differentiation potential to differentiate to all types of neural cells. By “effective amount of Pax6 protein”, we mean any amount of Pax6 protein that that is sufficient to convert the ESCs or iPSCs to pNSCs. Preferably, approximately 0.1-10.0 μg/ml of Pax6 protein with short peptide conjugation to help protein permibilization is used. Most preferably, approximately 0.5-8.0 μg/ml of Pax6 protein with short peptide conjugation to help protein permeabilization is used (Zhou et al., Cell Stem Cell, 2009, 5:381-384).

Differentiation of Regional Neural Stem Cells from PNSC Population

In another embodiment, the present invention is a method of creating regional neural stem cells from a primate pNSC population. In one embodiment, overexpression of Pax6 in primate pNSCs is controlled by an inducible promoter, and overexpression of Pax6 is turned off to induce differentiation from the pNSCs. Pax6⁺/Sox1⁻ pNSCs will express Sox1 in response to the down-regulation of Pax6, and further differentiation can be achieved. U.S. application Ser. No. 10/928,805, which has been issued as U.S. Pat. No. 7,588,937, discloses methods for directed differentiation of neural cells from Pax6⁺/Sox1⁻ pNSCs (incorporated herein).

Creation of Primitive Primate Neural Stem Cell Population from Regional Neural Stem Cells

In another embodiment, the present invention is a method of creating primate pNSCs from regional NSCs.

In one specific embodiment, the cells are created as follows: cortical (regional) NSCs, which do not have the potential to generate spinal cord neurons, are infected with Pax6 inducible lentivirus. Pax6 is then overexpressed in the cells through doxycycline treatment. The cortical NSCs are reprogrammed to pNSCs as the cells re-exhibit the potential to generate spinal cord neurons in response to retinoid acid due to Pax6 overexpression. Of course, one could use the method with any regional NSCs.

In other embodiments, overexpression of Pax6 is achieved by infection with other viruses, plasmid transfection, recombinant protein incubation or signaling/small molecule treatment.

Additional Embodiments

In another embodiment, the present invention is a method of increasing/decreasing Pax6 transcriptional activity, stability and its physiological function for generation, maintaining, reprogramming of pNSCs. In one embodiment, one can increase or decrease Pax6 transcriptional activity via regulation of kinases/phosphatases of Pax6 (Yan et al., J Biol Chem, 2007, 282:13954-13965; Kim et al., J Biol Chem, 2006, 281:7489-7497; Mikkola et al., J Biol Chem, 1999, 274:15115-15126). In addition, it has been reported that Pax6 stability can also be regulated by protesome-degradation pathway and mutation at certain Pax6 residues modulates protein proteolysis sensitivity (Tuoc et al., Genes Dev, 2008, 22:1972-1986; D'Elia et al., Eur J Hum Genet, 2006, 14:744-751). The preliminary research through transgenic analysis by the inventors has identified specific amino acid residues in the Pax6 protein which upon phosphorylation will either accelerate or block degradation of Pax6 protein. The inventors envision that one can use Pax6 mutants, kinases or phosphatases to regulate the protein stability of Pax6, thus regulating the stem cell fate.

In another embodiment, the present invention is a method of suppressing tumor formation in stem cell transplants by suppressing Pax6 expression. As mentioned earlier, transplantation of hESC-differentiated neural derivatives often resulted in over-growth of the grafts (Roy et al., Nat. Med., 2006, 12: 1259-1268; Sonntag et al., Stem Cells, 2007, 25: 411-418). Because Pax6-expressing pNSCs are present in the culture for transplantation, down-regulating Pax6, e.g. through infection with lentivirus coding Pax6 RNA interference (RNAi) would result in death of pNSCs or differentiation of pNSCs to neurons. Thus, tumorigenic tendency or overgrowth of hESC derivative transplants may be prevented by suppressing Pax6 expression. Suppression of Pax6 expression can be achieved many ways, e.g. through RNAi mediated Pax6 knockdown, blockage of endogenous Pax6 production and accelerating Pax6 degradation. Alternatively, small molecules, proteins or RNAi that interfere with Pax6 activity and its downstream effects can be used. Briefly, corresponding kinases, phosphatases or other proteins related to Pax6 activity or stability modulation can be overexpressed in the cells prior to transplantation to minimize Pax6 function. Alternatively, signaling/small molecules, which regulate those kinases, phosphatases or other proteins, can be applied directly to cells. Similar to overexpression of Pax6, this can be achieved by infection with other viruses, plasmid transfection, recombinant protein incubation or signaling/small molecule treatment.

In another embodiment, the present invention is a method of treating brain tumors by suppressing Pax6 expression or function. It is known that some brain tumors result from overgrowth of pNSCs. Targeting Pax6 would be an efficient and safe way to control these brain tumors by causing cells to die or differentiate to neurons. Suppression of Pax6 can be achieved by viruses, plasmids or synthesized double strand RNA mediated Pax6 knockdown in the brain tumors. Suppression of Pax6 can also be achieved by targeting kinases, phosphatases or other related proteins as well as signaling/small molecules systematically or locally as described above.

EXAMPLES Example 1

In Example 1, we show that Pax6 is uniformly expressed in pNSCs of human fetuses and those differentiated from human embryonic stem cells (hESCs). This is in contrast to the later expression of Pax6 in restricted mouse brain regions. Knockdown of Pax6 blocks pNSC specification from hESCs. Overexpression of either Pax6a or Pax6b, but not Pax6ΔPD, triggers hESC differentiation. However, only Pax6a converts hESCs to pNSCs. In contrast, neither loss nor gain of function of Pax6 affects mouse pNSC specification. Both Pax6a and Pax6b bind to pluripotent gene promoters but only Pax6a binds to pNSC genes during human pNSC specification. These findings indicate that Pax6 is a transcriptional determinant of the human pNSC and suggest that Pax6a and Pax6b coordinate with each other in determining the transition from pluripotency to the pNSC fate in humans by differentially targeting pluripotent and pNSC genes.

Introduction

In mammals, the stepwise cell fate transition during early embryonic development is orchestrated by sequential activation/inactivation of lineage-determining transcription factors (Yamanaka et al., Dev. Dyn., 2006, 235:2301-2314). Oct4, Sox2, and Nanog are required for maintaining pluripotency of the inner cell mass (ICM) or the epiblast in a blastocyst embryo (Avilion et al., Genes Dev., 2003, 17:126-140; Chambers et al., Cell, 2003, 113:643-655; Mitsui et al. Cell, 2003, 113:631-642; Nichols et al., Cell, 1998, 95:379-391). Differentiation of the ICM to extraembryonic tissues is governed by Cdx2 and Gata6, transcription factors that repress pluripotency while inducing genes of the trophectoderm and extraembryonic endoderm, respectively (Jedrusik et al., Genes Dev., 2008, 22:2692-2706; Koutsourakis et al., Development, 1999, 126:723-732.; Niwa et al., Cell, 2005, 123:917-929). After the formation of extraembryonic tissues, the pluripotent epiblasts are converted to three germ layers during gastrulation, but how these processes are regulated remains unknown.

One of the best-studied processes during gastrulation, pNSC specification, is at the center of developmental biology. Studies in lower vertebrates, including frogs and chicks, indicate that many transcription factors are involved in pNSC specification, including zinc finger proteins, Sox family, Otx family, and helix-loop-helix transcription factors (Mizuseki et al., Development, 1998, 125:579-587; Nakata et al., Proc. Natl. Acad. Sci. USA, 1997, 94:11980-11985; Rex et al., Dev. Biol., 1997, 271:439-466; Sheng et al. Cell, 2003, 115:603-613). To date, it is unclear which transcription factor is responsible for the conversion from pluripotent cells to pNSC in mammals. The most promising factor is Sox1, because its expression pattern parallels pNSC formation in mouse (Bylund et al., Nat. Neurosci., 2003, 6:1162-1168; Pevny et al., Development, 1998, 125:1967-1978). However, Sox1-knockout mice do not exhibit severe brain deficits, probably because of compensation by other Sox members (Nishiguchi et al. Genes Dev., 1998, 12:776-781). Similarly, the transcriptional determinant for human pNSC specification is unknown. The failure in identifying mammalian transcriptional determinants underlying pNSC specification is at least partly due to the lack of model systems that permit easy genetic manipulation and direct observation of developmental processes. Embryonic stem cells (ESCs), derived from the ICM or epiblast, differentiate to cells/tissues of the three germ layers according to developmental principles (Murry and Keller, Cell, 2008, 132:661-680; Stern, Development, 2005, 132:2007-2021; Zhang, Brain Pathol., 2006, 16:132-142). When human ESCs (hESCs) are differentiated toward the neural fate under a chemically defined medium in the absence of growth factors, pNSCs appear around day 6-8 and form neural tube-like rosettes at day 14 with corresponding gene expression patterns (Li et al., Nat. Biotechnol., 2005, 23:215-221; Pankratz et al., Stem Cells, 2007, 25:1511-1520; Zhang et al., Nat. Biotechnol., 2001, 19:1129-1133; Zhang and Zhang, Methods Mol. Biol., 2010, 584:355-366). This differentiation process resembles in vivo development of the neural plate and neural tube, and it therefore represents a useful tool for studying the molecular underpinnings of human pNSC specification (Zhang, Brain Pathol., 2006, 16:132-142).

During hESC neural differentiation, the pNSCs do not express Sox1, the earliest marker of pNSC in mouse embryos or in pNSC differentiated from mouse ESCs (mESCs) (Li et al., Nat. Biotechnol., 2005, 23:215-221; Pankratz et al., Stem Cells, 2007, 25:1511-1520; Pevny et al., Development, 1998, 125:1967-1978; Suter et al., Stem Cells, 2008, 27:49-58; Ying et al., Nat. Biotechnol., 2003, 21:183-186). Instead, Pax6, a paired box (Pax) transcription factor expressed in region-specific neural progenitors after neural tube closure in mouse (Schmahl et al. Acta Neuropathol., 1993, 86:126-135; Walther and Gruss, Development, 1991, 113:1435-1449), is uniformly expressed in hESC-derived pNSCs (Li et al. Nat. Biotechnol., 2005, 23:215-221; Pankratz et al., Stem Cells, 2007, 25:1511-1520). These observations raise an intriguing possibility that Pax6 may play a novel role in human pNSC specification. Three isoforms of Pax6 have been identified. The canonical Pax6a harbors two DNA binding domains, the paired domain (PD) and homeodomain (HD), and a prolineserine-threonine (PST)-rich transactivation domain. Pax6b is a spliced variant of Pax6, which is produced by insertion of 14 amino acids (exon5a) into the PD, thus conferring different DNA binding specificity (Epstein et al., Genes Dev., 1994, 8:2022-2034; Kozmik et al., EMBO J., 1997, 16:6793-6803; Walther and Gruss, Development, 1991, 113:1435-1449). The third isoform of Pax6 (Pax6ΔPD) lacks the paired domain. Both Pax6a and Pax6b are expressed in the brain, whereas Pax6ΔPD is identified only in eye and olfactory bulb (Kim and Lauderdale, Dev. Biol., 2006, 292:486-505). In rodents, Pax6 is essential for the development of several organ systems, including eye, pancreas, and cerebrum (Chi and Epstein, Trends Genet., 2002, 18:41-47).

Results

Pax6 is Uniformly Expressed in Early Human, but not Mouse, pNSCs.

During mouse development, Pax6 is first detected in neural progenitors of the developing forebrain at E8.5-E9.5, 1 day after the formation of Sox1-expressing neuroectoderm (NE) cells within the neural plate/tube (Bylund et al., Nat. Neurosci., 2003, 6:1162-1168; Pevny et al., Development, 1998, 125:1967-1978; Walther and Gruss, Development, 1991, 113:1435-1449). However, NE cells differentiated from various hESC lines (H1, H9, H13, HSF1, HSF6) and induced pluripotent stem cells (iPSCs) under different conditions uniformly express Pax6 while Sox1 are still negative (Gerrard et al., Stem Cells, 2005, 23:1234-1241; Hu et al., Proc. Natl. Acad. Sci. USA, 2010, 107:4335-4340; Li et al., Nat. Biotechnol., 2005, 23:215-221; Pankratz et al., Stem Cells, 2007, 25:1511-1520; Wu et al., Proc. Natl. Acad. Sci. USA, 2010, 107:5254-5259; Yao et al., Proc. Natl. Acad. Sci. USA, 2006, 103:6907-6912). Importantly, the Pax6-expressing NE cells can be readily patterned to region-specific, Sox1-expressing neural progenitors, which will give rise to various neuronal subtypes, including dorsal and ventral forebrain, midbrain, spinal cord, and retinal cells (Li et al., Nat. Biotechnol., 2005, 23:215-221, Li et al., Development, 2009, 136:4055-4063; Meyer et al., Proc. Natl. Acad. Sci. USA, 2009, 106:16698-16703; Pankratz et al., Stem Cells, 2007, 25:1511-1520; Yan et al., Stem Cells, 2005, 23:781-790; Zhang et al., Nat. Biotechnol., 2001, 19:1129-1133). This suggests that the early Pax6-expressing human NE cells represent a primitive state, i.e., the early Pax6-expressing human NE cells are pNSCs.

We thus hypothesized that Pax6 may play a unique role in NE specification besides regional patterning in human. Western blotting analysis revealed that Pax6 was detectable six days after hESC differentiation, whereas Sox1 started to be detected around day 14 (FIG. 1A). This was confirmed by immunostaining, showing that Pax6, but not Sox1, was expressed in pNSCs at day 8 of differentiation from the H1 and H9 hESC lines as well as a human iPSC line (FIG. 2). In contrast, Pax6 was not detected until 2-3 days after Sox1 expression during mouse ESC neural differentiation (FIG. 1B), consistent with previous reports (Bylund et al., Nat. Neurosci., 2003, 6:1162-1168; Suter et al., Stem Cells, 2008, 27:49-58). It is also noteworthy that both Pax6a and Pax6b, but not Pax6ΔPD, were expressed in human pNSCs, as confirmed by an antibody recognizing the C-terminus of Pax6 (shown in Figures S1B-S1D in Zhang et al. 2010, which is incorporated by reference; Kim and Lauderdale, Dev. Biol., 2006, 292:486-505).

Validation analysis in human fetal tissues (shown in Figure S1E in Zhang et al. 2010, which is incorporated by reference) revealed that at E18 (Carnegie stage 8-9), when the neural plate begins to form, Pax6, but not Sox1, was detected in the single-layered NE cells that were also Sox2 positive (FIG. 1C). This expression pattern was retained at E21 (Carnegie stage 10), in which the neural plate becomes pseudo-multiple layered. By the time that forebrain and midbrain have already been clearly demarcated at E26 (Carnegie stage 11-12), Pax6 was now restricted to the forebrain and part of the spinal cord but absent in the midbrain whereas both Sox1 and Sox2 were expressed in all NE cells (FIG. 1C). Our previous study showed that pNSCs differentiated from rhesus monkey ESCs also exhibited Pax6 expression (Pankratz et al., Stem Cells, 2007, 25:1511-1520). Consistent with the in vitro observations, pNSCs of rhesus monkey fetuses uniformly expressed Pax6, but not Sox1 (FIG. 3).

In contrast to primates, Sox1 and Sox2 were highly expressed in the mouse neural plate at E8 whereas Pax6 was not expressed (FIG. 1D). At E10.5, Pax6 was expressed in the dorsal forebrain and spinal cord, but not in the midbrain, whereas Sox1 and Sox2 were ubiquitously expressed in all NE cells (FIG. 1D).

Thus, Pax6 is expressed by human pNSCs but not mouse pNSCs, suggesting a potential distinct role of Pax6 in human NE specification.

Pax6 is Required for NE Specification from hESCs.

We then built ESC lines that constitutively express RNAi for Pax6 (targeting the homeodomain sequence and thus all three isoforms) or luciferase (Luc, as a control) through lentiviral infection (shown in Figure S2A in Zhang et al. 2010, which is incorporated by reference), and the knockdown efficacy was confirmed by western blotting (shown in FIG. 2A in Zhang et al. 2010, which is incorporated by reference) and RT-PCR (shown in FIGS. 7A and 7B in Zhang et al. 2010, which is incorporated by reference).

After ten days of neural differentiation under our chemically defined conditions, hESC-derived pNSCs with Luc RNAi presented typical columnar pNSC morphology and organized into early rosettes (Pankratz et al., Stem Cells, 2007, 25:1511-1520; Zhang et al., Nat. Biotechnol., 2001, 19:1129-1133). Noticeably, differentiating hESCs with Pax6 RNAi remained as round aggregates formed by round cells but not migrating columnar cells (shown in FIG. 2C in Zhang et al. 2010, which is incorporated by reference). Consistent results were obtained with different lines (with or without GFP) and different batches of differentiation, indicating that the knockdown phenotype was not due to asynchronized differentiation or different viral integration.

The lack of columnar pNSCs after Pax6 knockdown indicates failure of NE differentiation. Microarray analyses, by means of mRNA pooled from different transgenic lines, showed that about 500 genes were up- or down-regulated more than 5-fold in the Luc RNAi control line after 6 days of differentiation (shown in FIG. 2D in Zhang et al. 2010, which is incorporated by reference). Consistent with our previous report (Pankratz et al., Stem Cells, 2007, 25:1511-1520), the down-regulated genes were related to ESC/epiblast (e.g., Oct4, Nanog, and Myc) and the up-regulated genes (Lhx2, Six3, Six6, Lmo3, Meis2, N-cadherin, FGF8, FGF9, Delta like 1 homolog, and Wnt5b) were associated with the early NE (summarized in Tables S1 and S2 in Zhang et al. 2010, which is incorporated by reference). In contrast, fewer genes were up- or down-regulated in the Pax6 knockdown cells no matter what threshold (fold change) was set (shown in FIG. 2D in Zhang et al. 2010, which is incorporated by reference). The 50 most up- and down-regulated genes during differentiation of the control ESCs were less changed in the Pax6 knockdown lines (shown in FIG. 2E in Zhang et al. 2010, which is incorporated by reference), which were confirmed by qRT-PCR (shown in FIG. 7B in Zhang et al., 2010). Thus, cells with Pax6 knockdown largely retained pluripotent gene expression and had much less NE gene expression. Cell cycle analyses revealed no differential cell death or proliferation after Pax6 knockdown (shown in Figures S6A-S6C in Zhang et al., 2010). Therefore, Pax6 knockdown prevents hESCs from differentiation, thus trapping them in the pluripotent state.

After another 1-2 weeks of differentiation, NE cells from the Luc RNAi group readily formed NE aggregates and generated βIII-tubulin-positive neurons. In contrast, cells with Pax6 knockdown under the same conditions rarely formed NE spheres and they failed to differentiate into neurons in adherent culture (shown in FIGS. 2B and 2C in Zhang et al., 2010). These data also suggest that cells derived from Pax6 RNAi lines are not properly developed to the NE stage.

To exclude the possibility that the requirement of Pax6 in NE specification was due to our differentiation protocol, we adopted a new neural differentiation protocol through dual SMAD signaling inhibition (Chambers et al., Nat. Biotechnol., 2009, 27:275-280). Again, knockdown of Pax6 severely blocked pluripotent gene down-regulation and NE gene up-regulation even with the addition of BMP inhibitors (shown in Figure S2B in Zhang et al., 2010).

To further exclude the possibility of cell culture artifact, undifferentiated hESCs were injected subcutaneously into severe combined immunodeficient (SCID) mice to produce teratomas, an in vivo system allowing ESC to differentiate into multilineages including neural tissues. Teratoma generation efficiency and size were comparable in both control and Pax6 knockdown groups. NE rosettes, revealed by hematoxylin and eosin (H&E) staining and confirmed by immunostaining for Sox1 and Sox2, were frequently observed in teratomas formed by hESCs with Luc RNAi but rarely in the Pax6 RNAi group (shown in FIGS. 3A and 3B in Zhang et al., 2010). Nevertheless, mesoderm (cartilage) and endoderm (gut epithelium) derivatives were observed in both Luc and Pax6 knockdown tumors (shown in FIG. 3A in Zhang et al., 2010). Western blotting analyses of individual teratomas validated that the levels of neural transcription factors Sox1 and Sox2 drastically decreased in the Pax6 knockdown tumors, whereas the endodermal marker, alpha-fetoprotein (AFP), and epidermal marker, cytokeratin, were expressed at similar levels in both groups (shown in FIG. 3C in Zhang et al., 2010). These data indicate that the requirement of Pax6 for human NE specification is not a culture artifact and Pax6 is probably a potential downstream factor of extracellular neural inducers during human NE specification.

Pax6 is not Required for Mouse Ne Specification.

The opposite temporal expression pattern of Pax6 and Sox1 in human versus mouse suggests a differential role of Pax6 in NE specification in these two species. To test this hypothesis, we infected the D3 and Sox1/GFP reporter (Ying et al., Nat. Biotechnol., 2003, 21:183-186) mESCs with Pax6 or Luc RNAi lentiviruses (the RNAi targeting sequence is identical between human and mouse) and confirmed the knockdown efficiency by western blotting (shown in Figure S2E in Zhang et al., 2010). Differentiation to Sox1-expressing mouse NE cells, indicated by GFP, was readily observable at day 6 and reached a peak at day 9-10, consistent with western blotting analyses (FIG. 1B). However, knockdown of Pax6 did not affect the Sox1 level as evaluated by fluorescent microscopy or FACS, suggesting that Pax6 is not necessary for mouse NE specification (shown in Figures S2C and S2D in Zhang et al., 2010). Western blotting with the naive mESCs (D3 line) confirmed that neither Pax6 nor Luc RNAi altered the expression of Sox1 (shown in Figure S2E in Zhang et al., 2010). The Pax6 RNAi-expressing mouse NE cells further differentiated to neurons with similar efficiency as the Luc RNAi control (shown in Figure S2F in Zhang et al., 2010).

The side-by-side comparison of Pax6 RNAi effects on human versus mouse ESC neural differentiation strongly suggests that Pax6 is a crucial transcription factor for NE specification in human, but not mouse.

Overexpression of Pax6 in hESCs Down-Regulates Pluripotent Gene Expression.

We next expressed Pax6a and Pax6b (with GFP fusion to the C terminus) in hESCs under the elongation factor (EF) 1α promoter through lentiviral infection (see Figure S1B in Zhang et al., 2010 for diagrams demonstrating the constructs). GFP expression was visible 30-40 hr after viral infection in both GFP- and Pax6-GFP-overexpressing cells with the highest GFP expression at day 4-5. Three days after infection, forced expression of GFP alone had no effect on Oct4 or Nanog expression, whereas overexpression of either Pax6a-GFP or Pax6b-GFP resulted in loss of Oct4 and Nanog expression even under the culture conditions that favored ESC maintenance (see FIGS. 4A and 4B in Zhang et al., 2010 for examples).

Pax6 is a transcription factor with three key functional domains. The paired domain (PD) and homeodomain (HD) are for DNA binding and the P/S/T-rich transactivation domain (PST) holds the transcriptional activity. Within the paired domain, there also includes two sub-domains, the PAI and RED domains. It is reasonable to hypothesize that Pax6 employ different DNA binding domains for different target gene promoter occupancy and the PST domain regulates the transcriptional activity of those genes. Through this, Pax6 can thus fulfill its various physiological functions, such as brain, eye and pancreas development.

Except for the HD, all of the major parts of the Pax6 molecule, including the paired domain and the PST domain, are required for the effect of Pax6 on hESC differentiation. Specifically, overexpression of Pax6ΔPD (FIG. 18) did not affect Oct4 or Nanog expression, indicating the requirement of the paired domain in down-regulating pluripotent genes. Further experiments with Pax6 mutants indicated that deletion of the N-terminal PAI domain (FIG. 16) or the PST transactivation domain (FIG. 20), but not the HD of Pax6 (FIG. 14), abrogated the effect of Pax6 in repressing Oct4 and Nanog. See Figure S3 in Zhang et al., 2010 for examples.

Overexpression of Pax6a but not Pax6b Directs hESCs to NE.

Although both Pax6a and Pax6b down-regulated pluripotent genes, it was not known whether the two Pax6 isoforms acted similarly on NE specification. By monitoring the hESC cultures daily, we discovered that, unlike the GFP control cells, the initially scattered Pax6a-GFP cells gradually aggregated in the hESC colonies (see FIG. 4C in Zhang et al., 2010 for demonstrations). Similar aggregation was observed in Pax6ΔEHD mutant (see Figure S3 in Zhang et al., 2010 for demonstrations). Eight days after lentiviral infection, Pax6a-positive cells exhibited an elongated columnar morphology and formed rosettes (see FIG. 4D in Zhang et al., 2010 for demonstrations), indicative of their neural identity. Interestingly, the inventors found that Pax6b-GFP-expressing cells migrated to the edge of the hESC colonies and eventually became large flat cells, giving a membranous appearance outside of the hESC colonies (see FIGS. 4C and 4D in Zhang et al., 2010 for demonstrations). By fluorescent microscopy, the inventors noticed kidney-like or horseshoe-shape large nuclei with two or more lobes in most Pax6b-GFP-positive cells (see FIG. 4D in Zhang et al., 2010 for demonstrations). The migration property, cell morphology, and multiploid nuclei suggest that the Pax6b-expressing cells have adopted a trophoblast-like fate.

Although forced expression of Pax6a down-regulated Oct4 and Nanog quickly, expression of another pluripotent factor, Sox2 (also a NE transcription factor), was retained (see FIG. 5A in Zhang et al., 2010 for demonstrations). The Pax6a-overexpressing cells also expressed fatty acid binding protein 7 (Fabp7) and N-cadherin (see FIGS. 5B and 5C in Zhang et al., 2010 for demonstrations), which are specifically expressed in NE cells. It should be noted that N-cadherin was distributed evenly on the membrane of the Pax6a-expressing cells. It is known that the pNSCs express N-cadherin evenly on the cell membrane whereas regional neural progenitors that express Sox1 and are polarized express N-cadherin on the lumen side (Pankratz et al., Stem Cells, 2007, 25:1511-1520). Hence, the specific expression pattern of N-cadherin in Pax6a-overexpressing cells indicates their pNSC state, which coincides with our finding that most Pax6a-positive cells were negative for Sox1. Occasionally, Sox1 was found in the Pax6a-positive cells. Interestingly, the Sox1-expressing cells always had lower Pax6a expression (see FIG. 5D in Zhang et al., 2010 for demonstrations).

In contrast to Pax6a, Pax6b-overexpressing cells showed no expression of any neural marker tested, confirming their nonneural identity. Furthermore, both Pax6a and Pax6b cells lacked expression of Brachyury and AFP, mesodermal and endodermal markers, respectively, or Gata6, an extraembryonic endodermal maker (data not shown).

Thus, although both Pax6a and Pax6b triggered hESC differentiation through down-regulation of pluripotent genes, only Pax6a directed the cells to a neural fate.

In contrast to the results seen with hESCs, overexpression of either Pax6a or Pax6b in mESCs neither changed the ESC morphology nor induced the formation of early rosettes. Overexpression of Pax6a or Pax6b in mESCs did not decrease Oct4 expression and the mESCs could be passaged continuously as normal ESCs (see Figures S4A and S4B in Zhang et al., 2010 for demonstrations). Therefore, the prominent ESC-differentiation and neural-inducing effects of Pax6 are unique to human ESCs.

Pax6a but not Pax6b Induces NE Gene Expression.

Expression of either Pax6a or Pax6b differentiates hESCs rapidly and this prevented us from establishing stable transgenic lines for biochemical studies. We therefore built inducible Pax6a, Pax6a-GFP, Pax6b-GFP, and GFP clonal hESC lines by using a lentivirus-based inducible system (Xia et al., Stem Cells, 2008, 26:525-533). Doxycycline treatment or induction of GFP expression did not alter the morphology and growth of hESCs. In contrast, induction of Pax6a-GFP expression in hESCs for 3-4 days trigged neural rosette formation in the ESC colony. We again found that Pax6b-GFP-overexpressing cells tended to localize in the periphery of the colony and they possessed the same kidney-like or horseshoe-shape nuclei as seen previously (data not shown). These results confirmed the observations made with constitutive Pax6-expressing cells that Pax6a, but not Pax6b, promotes pNSC specification.

To examine the dynamics of Pax6 effects, we performed qRT-PCR analyses after Pax6 was induced for 1, 3, or 5 days in ESC culture conditions. Consistent with microarray data (see FIG. 2E and Table S1 in Zhang et al., 2010, for demonstrations), neural differentiation of normal hESCs was accompanied by up-regulation of neural transcription factors including Lhx2, Six3, Six6, Lmo3, and Meis2 as well as neural-related signaling molecules, such as Fabp7, Lix1, Dlk1, Dach1, and N-cadherin at days 6 and 10 (see FIG. 6A in Zhang et al., 2010, for demonstrations). Induction of GFP expression did not alter the gene expression pattern in hESCs. Pax6a or Pax6a-GFP expression greatly induced those neural genes within 1-3 days, but not genes of extraembryonic lineages, mesoderm, endoderm, or epidermal tissues (see FIG. 6B in Zhang et al., 2010, for demonstrations). These results suggest that Pax6a induces neural gene expression and the fusion of GFP to Pax6 does not interfere with its function.

In animal studies, Pax6 is important for eye and pancreas development and brain patterning. RT-PCR analysis indicated that retinal (Crx, Chx10, and RPE65), mesoendodermal (Brachyury), and pancreatic (Sox17, Hnf1b, and Pdx1) genes or regional patterning genes (FoxG1, En1, Hoxb4, and Nkx2.1) were not induced by Pax6a (see Figures S5A-S5C in Zhang et al., 2010, for demonstrations), further supporting the pNSC specification effect of Pax6a. In contrast, overexpression of Pax6b-GFP did not induce NE gene expression or characteristic genes from other germ layers except Cdx2 (see FIG. 6B in Zhang et al., 2010, for demonstrations), a key factor for trophectoderm development. In this case, Cdx2 was not increased until 5 days after induction of Pax6b.

It is noteworthy that the pNSC-inducing effect of Pax6a is quick and robust. Even in the presence of Activin A and Bio (a GSK3β inhibitor), a condition that favors mesoendoderm differentiation (Kroon et al., Nat. Biotechnol., 2008, 26:443-452), Pax6a overexpression induced neural rosette formation within hESC colonies with concomitant elevated expression of NE genes and repressed mesoendodermal transcripts (see Figures S5D-S5F in Zhang et al., 2010, for demonstrations). These data suggest that Pax6 is an intrinsic regulator of human pNSC specification.

Pax6a and Pax6b Coordinate with Each Other to Specify the NE Fate.

Because both Pax6a and Pax6b were expressed during hESC NE differentiation (FIG. 1A) but overexpression of Pax6a alone was sufficient to convert hESCs to pNSC, we asked whether Pax6b was needed for pNSC specification. We selected one RNAi sequence targeting exon5a that can specifically knock down Pax6b (see FIG. 7A and Figure S2A in Zhang et al., 2010, for demonstrations). qRT-PCR showed that similar to knock down of both isoforms, specific knockdown of Pax6b reduced pluripotent gene down-regulation and neural gene up-regulation during normal NE differentiation, although at a modest level (see FIG. 7B in Zhang et al., 2010, for demonstrations). These results suggest that Pax6b is also required for human pNSC specification. Because overexpression of Pax6b cannot induce neural genes, this result suggests that the way Pax6b functions in human pNSC specification is through coordinating with Pax6a in down-regulation of pluripotent genes, which is a prerequisite for subsequent up-regulation of neural genes. In addition, the neural blocking effect was reproduced with two Pax6 RNAi constructs, ensuring that the phenotype was due to knock down of Pax6, but not off-target effects.

We then asked whether Pax6 can regulate lineage genes directly. Pax6a-GFP, Pax6b-GFP, and GFP lines were induced with doxycycline for 1 and 3 days, and chromatin immunoprecipitation (ChIP) analysis was performed to examine the binding of Pax6 to promoters of lineage-specific genes. GFP protein did not show any binding to the pluripotent genes or neural genes (data not shown). Both Pax6a and Pax6b were found to localize to the Oct4 and Nanog promoters (see FIG. 7C in Zhang et al., 2010 for demonstrations). Pax6 bound to the Nanog promoter one day after Pax6 was induced, earlier than it bound to the Oct4 promoter. This is consistent with the observation that Nanog was down-regulated earlier than Oct4 in normally differentiated cells. As expected, only Pax6a bound to the promoters of neural genes that were up-regulated after Pax6a expression, mostly at day three. In summary, both Pax6a and Pax6b bound to the promoters of pluripotent genes, corresponding to the downregulation of Oct4 and Nanog. Pax6a, but not Pax6b, occupied the promoters of neural genes, coinciding with the NE fate mediated by Pax6a.

Pax6 Overexpression Maintains Cells in pNSC State and Blocking Pax6 Expression in NSCs Leads to Cell Death or Differentiation into Neurons.

Maintaining of NSCs in a primitive state can be achieved by Pax6 overexpression and driving the cells out of the primitive state can also be achieved by shutting off Pax6 expression. As demonstrated by transgenic hESC lines in FIG. 4, after differentiation to pNSCs at day 10, induction and maintenance of Pax6 by doxycycline treatment for two weeks kept growth factor-independent proliferation and suppressed Sox1 expression. Three days after Dox removal, many cells began to express Sox1. In addition, the inducible transgenic overexpression/knockdown tool represents a useful strategy to control the cell fates.

It is noteworthy that Pax6b is also required for maintaining pNSCs. In forebrain dorsal NSCs, low level of Pax6 is also expressed together with Sox1. When we differentiate hESCs toward a neural fate, they will be faulted to a forebrain dorsal identity (Li et al., Development, 2009, 136:4055-4063). However, if Pax6b is knocked down as demonstrated by Pax6b RNAi hESC lines, these NSCs cannot be maintained in a primitive state and they terminally differentiate to certain migrating flat cells and neurons with some dead cells starting to detach from the culture surface (FIG. 5A). In another experiment where day 14 NSCs were transiently infected with Pax6 RNAi lentiviruses (targeting both Pax6a and Pax6b), we also found massive cell death and neuronal differentiation 3-4 days after virus infection (FIG. 5B). These data demonstrate that Pax6 (probably both a and b isoforms) is crucial for maintaining NSCs. Downregulation of Pax6 will thus drive NSCs to leave the primitive stage, and then drive neural progenitors to differentiate to neurons.

Discussion

Since the groundbreaking work by Spemann and Mangold, signaling pathways that lead to NE induction, including BMP inhibition and FGF activation, are now well established (Levine and Brivanlou, Dev. Biol., 2007, 308:247-256; Muñoz-Sanjuán and Brivanlou, Nat. Rev. Neurosci., 2002, 3:271-280; Stern, Development, 2005, 132:2007-2021, Stern, Curr. Opin. Cell Biol., 2006, 18:692-697). However, transcriptional networks that control NE specification are not well defined. Our present study provides evidence that Pax6 is both necessary and sufficient for pNSC specification from human but not mouse ESCs. This finding raises a question of how such a well-conserved protein acquired the novel function in human brain development over evolution. Furthermore, we discovered that the neural inductive function of Pax6 is achieved by its repression of pluripotent genes and activation of NE genes. Taken together with the unique differential effects of Pax6a and Pax6b, we propose that specification of epiblast or ESCs to an embryonic germ layer depends upon induction of the target germ layer genes and repression of pluripotent genes and possibly also genes of other germ layers (see FIG. 7D in Zhang et al., 2010 for demonstrations). This proposition opens the possibility for the existence of a determinant gene(s) for mesoderm and endoderm.

Pax6 is Necessary and Sufficient for Human pNSC Specification.

In this study, we have demonstrated that overexpression of Pax6, either constitutively or conditionally, converts hESCs to pNSCs, even under conditions that favor hESC maintenance or mesoendoderm differentiation. The pNSC identity was verified by the characteristic columnar cells that organize into early rosettes, loss of pluripotent gene expression, upregulation of NE genes, and lack of other germ layer markers. Knockdown of Pax6 blocks pNSC specification from hESCs not only in the teratoma assay, which allows spontaneous three-germ-layer differentiation in vivo, but also in our chemically defined NE differentiation system and a newly developed dual SMAD inhibition culture, both of which strongly promote hESC neural differentiation. These results, gathered from both gain of function and loss of function of Pax6 under opposing conditions, strongly indicate that Pax6 is an intrinsic determinant for the human pNSC fate. The fact that overexpression of Pax6 does not induce mesoendoderm and that knockdown of Pax6 does not inhibit mesoendodermal lineage differentiation excludes the possibility that Pax6 first promotes mesoendodermal differentiation which in turn induces neural differentiation. This is further supported by the result that dual SMAD inhibition by Noggin and SB431542 does not rescue the neural blocking effect when Pax6 is knocked down. Therefore, Pax6 is most probably a crucial downstream effector of neural inducers, such as BMP inhibitors.

Pax6-Mediated pNSC Specification Depends on Both Repression of Pluripotent Genes and Induction of NE Genes.

It is quite remarkable that a single transcription factor, Pax6, can act as a switch from proliferating hESCs to differentiating pNSCs. This is a direct cell fate conversion rather than an indirect process through promoting cell proliferation or survival of existing pNSCs in the hESCs (Schroeder, Nature, 2008, 453:345-351). First, hESCs, maintained under standard culture conditions, do not express Pax6, an early marker of human pNSCs now widely used. Second, overexpression or knockdown of Pax6 does not alter cell proliferation or survival (see Figure S6 in Zhang et al., 2010 for demonstrations). Third, time-lapse tracking reveals that once Pax6 is turned on, the cells become columnar pNSCs, migrate, and aggregate to form early rosettes (see Movies 51 and S2 in Zhang et al., 2010 for examples). Furthermore, at the molecular level, Pax6 binds to pluripotent genes and NE genes directly.

Removal of either the PAI domain, the whole PD or PST domain, all abrogates the function of Pax6 to differentiate hESCs to pNSC. However, the HD is not required for Pax6 induced pNSC specification, as deleting of this HD domain does not affect stem cell genes downregulation and pNSC generation. The same phenomenon has also been observed in a zebrafish study, which shows the HD is dispensable for Pax6 mediated pancreatic endocrine cell differentiation (Verbruggen et al., J Biol Chem, 2010, 285:13863-13873). In addition, it has been reported widely about a large number of Pax6 mutations, which caused aniridia and brain dysfunctions in humans. Furthermore, biochemistry analysis also demonstrates that phosphorylation/dephosphorylation of certain S/T amino acids can regulate Pax6 transcriptional activity (Yan et al., J Biol Chem, 2007, 282:13954-13965; Kim et al., J Biol Chem, 2006, 281:7489-7497; Mikkola et al., J Biol Chem, 1999, 274:15115-15126). These suggest that regulation of kinases/phosphatases of Pax6, mutating certain key residues of Pax6 or deleting certain Pax6 protein domains can be efficiently used to increase/decrease Pax6 transcriptional activity, stability and its physiological function. And these strategies can also be used for generation, maintaining, reprogramming of pNSCs and controlling brain tumors.

Both Pax6a and Pax6b bind to promoters of pluriptoent genes, including Oct4 and Nanog, and repress their expression whereas only Pax6a binds to NE gene promoters and activates NE genes. Therefore, the pNSC fate-determining role of Pax6 is achieved through coordination of Pax6a and Pax6b in preventing hESC self-renewal, thus initiating their differentiation and inducing the cells toward the pNSC fate by Pax6a. Suppression of pluripotent factors alone is not sufficient for differentiating ESC/epiblast to pNSCs. This is demonstrated by the fact that overexpression of Pax6b, which does not possess neuralinducing activity, drives hESCs out of the stem cell state but these cells turn into trophoblast. This phenomenon is reminiscent of the extraembryonic outcome of ESCs with knockdown of Oct4, Nanog, or Sox2 (Chew et al., Mol. Cell. Biol., 2005, 25:6031-6046; Fong et al., Stem Cells, 2008, 26:1931-1938; Hay et al., Stem Cells, 2004, 22:225-235; Hyslop et al., Stem Cells, 2005, 23:1035-1043; Matin et al., Stem Cells, 2004, 22:659-668; Zaehres et al., Stem Cells, 2005, 23:299-305). Thus, repression of pluripotent genes initiates the differentiation process but it alone is not sufficient for embryonic germ layer differentiation. Pax6a is probably the key inductive signal for the pNSC fate. Indeed, Pax6a binds to a set of downstream neural genes, which corresponds to the neural phenotypes. Pax6b, though by itself not a direct neural inducer, potentiates the neural inductive effect of Pax6a through collaboration with Pax6a for sufficient repression of pluripotent genes, which is a prerequisite for induction of neural genes (see FIG. 7D in Zhang et al., 2010 for demonstrations).

The pNSC Specification Role of Pax6 is Unique to Primates.

The Pax6 protein is highly conserved. It plays critical roles in the development of eyes and pancreas and patterning of neural progenitors across species (Chi and Epstein, Trends Genet., 2002, 18:41-47). Indeed, the expression pattern of Pax6 in the developing human nervous system (after brain regions are formed) is very similar to that in other model systems, including mouse, frog, chick, and fish (Amirthalingam et al., Biochem. Biophys. Res. Commun., 1995, 215:122-128; Goulding et al., Development, 1993, 117:1001-1016; Schlosser and Ahrens, Dev. Biol., 2004, 271:439-466; Walther and Gruss, Development, 1991, 113:1435-1449). We have also confirmed that Pax6 is essential for patterning human NE cells to ventral spinal progenitors and dorsal telencephalic progenitors (Li et al. Nat. Biotechnol., 2005, 23:215-221; Li et al., Development, 2009, 136:4055-4063). Our side-by-side comparison of Pax6 expression and function between mouse and human revealed a novel role of Pax6 in early human, but not mouse, pNSC specification. Considering the similar expression pattern of Pax6 in early rhesus monkey fetuses, this pNSC specification role of Pax6 probably is unique to primates. This finding raises a question as to why the classical transcription factor, with 100% amino acid sequence homology between mouse and human, acquires a new role in human brain development. The brain, especially the forebrain, is the most highly evolved structure in either size or complexity among species (Dorus et al., Cell, 2004, 119:1027-1040; Kaas, Curr. Biol., 2006, 16:R910-R914; Rakic, Nat. Rev. Neurosci., 2009, 10:724-735). Corresponding to the increasing size of the forebrain, some neural transcription factors, especially anterior transcription factors Sox2 and Otx2 whose expression is restricted to the neural lineage in lower vertebrates, are now found at earlier developmental stages in mammals, even in the inner cell mass and the epiblast of the embryo (Avilion et al., Genes Dev., 2003, 17:126-140; Simeone et al., EMBO J., 1993, 12:2735-2747). The cerebrum in primates, especially in human, is proportionally larger and more complex in neural circuitry than in rodents (Dorus et al., Cell, 2004, 119:1027-1040; Kaas, Curr. Biol., 2006, 16:R910-R914; Rakic, Nat. Rev. Neurosci., 2009, 10:724-735). We and others have also found that under similar culture conditions without exogenous morphogens, hESC-derived NE cells tend to generate cortical glutamatergic neurons whereas mouse NE are inclined to generate ventral GABAergic neurons (Gaspard et al. Nature, 2008, 455:351-357; Li et al., Development, 2009, 136:4055-4063). We speculate that early Pax6 expression might be the first step to ensure a large cerebrum in primates. Further studies to identify target genes of Pax6 during NE specification may well shed light on the evolutionary complexities of our human brain. Our finding also raises the question of what would be the determinant gene for the NE fate in mouse or other animals. Comparison of our gene profiles with available database of mouse NE (Aiba et al., Stem Cells, 2006, 24:889-895) revealed profound differences in gene expression between human and mouse NE, some of which are presented in Figure S1G in Zhang et al., 2010. While this comparison corroborates our present finding, it indicates a need of uncovering the long-sought NE determinant in animals.

Significance of Pax6 Overexpression in iPSCs

Overexpression of Pax6 or its derivatives will be an efficient way to convert human iPSCs to pNSCs. It is known that hESCs and human iPSCs employ identical transcriptional programs during neural differentiation (Zhang et al., Cell Stem Cell, 2010, 7:90-100; Hu et al., Proc Natl Acad Sci USA, 2010, 107:4335-4340). Not only do human iPSCs use the same transcriptional factors as hESCs to generate neuroepithelia and functionally appropriate neuronal types, iPSCs also follow the same developmental time course as hESCs in response to the same set of morphogens (Zhang et al., Cell Stem Cell, 2010, 7:90-100). Consistent with what is known, we showed above, with various human ESC lines and human iPSCs, that pNSCs differentiated from both hESCs and iPSCs are Pax6+/Sox1−.

Overexpression of Pax6 or its derivatives may be an efficient way to convert human iPSCs to pNSCs. When applied with hESC differentiation protocol, human iPSCs do show lower efficiency in neural differentiation than hESCs. Using our neural differentiation protocol, human ESCs always end up with over 90% pNSCs after 8-10 days of differentiation, while neural differentiation efficiency of human iPSCs, in most cases, is less than 50%) (Hu et al., Proc Natl Acad Sci USA, 2010, 107:4335-4340). We note lack of Pax6 expression at the initiation stage of pNSCs specification in iPSCs (data not shown) and believe the low neural differentiation efficiency of human iPSCs is rooted from inefficient activation of endogenous Pax6 expression when hESC neural differentiation protocol is used.

Example 2 Genes Highly Enriched in pNSCs but Downregulated in Regional NSCs

pNSCs differ from regional NSCs in several aspects. For example, pNSCs are Pax6+/Sox1−, while regional NSCs are Sox1+. In addition, pNSCs have the potency to be patterned to all kinds of neural cells with different regional identities, but regional NSCs are fixed to certain regional identities. In order to further characterize the differences between pNSCs and regional NSCs, we compared the gene expression profiles of day10 pNSCs and day17 forebrain dorsal NSCs using an affymetrix mircroarray (Pankratz et al., Stem Cells, 2007, 25:1511-1520; Li et al., Development, 2009, 136:4055-4063). Genes which were expressed in pNSCs but their expression was downregulated for at least 4 fold in regional NSCs are listed below in Table 1. These genes will thus be served as representative genes to separate pNSCs and regional NSCs. They are also candidate genes potentially useful for pNSCs reprogramming.

TABLE 1 Affymetrix Physisological Probes Genes Functions 211267_at HESX homeobox 1 transcription and DNA (HESX1) binding 208449_s_at fibroblast growth factor 8 signal transduction and (FGF8) growth factor activity 220448_at potassium channel, ion channel activity subfamily K, member 12 (KCNK12) 213661_at peptidase domain proteolysis containing associated with muscle regeneration 1 (PAMR1) 219545_at potassium channel ion channel activity tetramerisation domain containing 14 (KCTD14) 204951_at ras homolog gene family, small GTPase mediated member H (RHOH) signal transduction 206209_s_at carbonic anhydrase IV carbonate dehydratase (CA4) activity 1552520_at transmembrane protein autophagy 74 (TMEM74) 208893_s_at dual specificity inactivation of MAPK phosphatase 6 (DUSP6) activity 205578_at receptor tyrosine kinase- nucleotide binding and like orphan receptor 2 kinase activity (ROR2) 228335_at claudin 11 (CLDN11) cell adhesion 219955_at LINE-1 type transposase N/A domain containing 1 (L1TD1) 209466_x_at pleiotrophin (PTN) phosphoprotein phosphatase inhibitor activity and growth factor activity 243161_x_at zinc finger protein 42 DNA binding and homolog (ZFP42) transcriptional activity 213201_s_at troponin T type 1 protein binding (TNNT1)

Example 3 Overexpression of Pax6 in Regional Neural Stem Cells Reverts the Regional NSCs to pNSCs

Transcription factors have the potential to reverse the cell differentiation programs or trans-convert one cell fate to another. For example, Oct4, Sox2, KIM and c-Myc are the four typical transcription factors for reprogramming iPSCs (Yu et al., Science, 2007, 318: 1917-1920; Takahashi et al., Cell, 2007, 131: 861-872). In addition, Ascl1, Brn2 (also called Pou3f2) and Myt1I are sufficient to directly convert fibroblasts to neurons (Vierbuchen et al., Nature, 2010, 463:1035-1041).

We hypothesized that regional NSCs can also be reprogrammed to pNCSs through forced expression of transcription factor(s) and Pax6 may be the critical factor given its unique role in specifying pNSCs. To test this hypothesis, we derived cortical NSCs from human fetal cortex (Schneider et al., Hum Mol Genet, 2007, 16:651-666; Wright et al., Exp Cell Res, 2006, 312:2107-2120). These regional NSCs are fate-restricted and do not have the potential to generate spinal cord progenitors (Wright et al., Exp Cell Res, 2006, 312:2107-2120). As demonstrated in FIG. 6, the cortical NSCs with GFP overexpression do not grow well after retinoid acid challenging for five days. This indicates that these regional NSCs are fixed to the cortical fate and that they do not accommodate to the caudalization signal. This result is further supported by the fact that retinoid acid treatment failed to upregulate HoxB4, a classic spinal cord gene, in the cortical NSCs.

In contrast, infecting the cortical NSCs with inducible lentiviruses, Pax6a and Pax6b followed by doxycycline treatment to overexpress both isoforms of Pax6 in these regional NSCs endows the cells with multi-potency. These cortical-fate fixed regional NSCs are now responsive to retinoid acid. They expand well and express HoxB4 after five days of retinoid acid treatment.

These data suggest that Pax6 expression reprograms regional NSCs to an earlier pNSC state, because only pNSCs are multi-potent and can be directed to different regional fates, such as responding to retinol acid and generating spinal cord NSCs.

Example 4 Overexpansion of pNSCs in Transplants Causes Tumor Formation

hESCs and human iPSCs derived tissues or cell types are invaluable sources for replacement therapy. However, transplantation of stem cell derived neural cells is often ends up with over-growth of the grafts (Roy et al., Nat. Med, 2006, 12: 1259-1268; Sonntag et al., Stem Cells, 2007, 25: 411-418).

We checked our cultures used for future transplantation in Parkinson's disease animal models and found that there always were some Pax6 positive NSCs (FIG. 7A). After transplantation, we frequently identified tumors surrounding the cell injection spots. As demonstrated by FIG. 7B, the tumors were comprised of Pax6+/Sox1− pNSCs. These data suggest that the pNSCs within the transplants gradually lost of control and over-expand to form tumors. Down-regulation of Pax6 to drive the cells out of primitive state and ultimately differentiate the cells to neurons would be an efficient and safe way to eliminate tumor occurrence.

Example 5 A Non-Genetic Means to Regulate Pax6 Expression

The inventors envision that development of non-genetic strategies to regulate Pax6 expression may facilitate future clinical translation. One way to regulate transcription factors like Pax6 is to modulate protein degradation. We discovered that phosphorylation of certain serine residue blocks or enhances Pax6 degradation.

Using the HEK cells that express the mutant Pax6 constructs with a GFP tag, the inventors identified molecules that block Pax6 degradation (aiming at maintaining Pax6 level and the primitive state of NSCs, FIG. 8A) or promote Pax6 degradation (thus removing Pax6 and exiting cell cycle of NSCs, FIG. 8B) in their initial screening on library of pharmaceutically active compounds (LOPAC, 64,000 compounds), which were verified by dose-dependent effect. This will allow one to regulate Pax6 by non-genetic means, thus controlling the maintenance of and reprogramming of differentiated neural cells to the primitive state of NSCs or promote NSC differentiation thus lower the risk of tumor formation after transplantation.

Example 6 Experimental Procedures for the Previous Examples

Culture and Maintenance of Mouse and Human ESCs

Protocols for culturing and maintenance of mouse and human ESCs are well known in the art. Briefly, hESCs (H9 and H1 lines, passages 18-35) were provided by the WiCell Institute (Madison, Wis.) and were cultured on irradiated mouse embryonic fibroblasts (MEFs) as previously described (Zhang et al., Nat. Biotechnol., 2001, 19:1129-1133; Zhang and Zhang, Methods Mol. Biol., 2010, 584:355-366).

Similarly, methods to generate iPSCs are also well-known in the art. In examples disclosed above, human iPSCs were generated from skin fibroblasts by overexpressing Oct4, Sox2, Klf4, and c-Myc through retroviral infection (Hu et al., Proc. Natl. Acad. Sci. USA, 2010, 107:4335-4340). The standard protocol was also described by Park et al. (Nat Protoc, 2008, 3:1180-1186).

Mouse ESCs (D3 line and Sox1/GFP reporter line 46C) were cultured on MEF supplemented with 50% medium conditioned by Buffalo rat liver cells (BRL-CM).

Neural Differentiation from Human and Mouse ESCs

Neural differentiation of hESCs was performed according to a published protocol (Zhang et al. Nat. Biotechnol., 2001, 19:1129-1133; Zhang and Zhang, Methods Mol. Biol., 2010, 584:355-366). For mESC neural differentiation, half a million cells were suspended in DMEM-F12/neurobasal medium (1:1 DMEM-F12/neurobasal medium, 13 N2 neural supplement, 13 lipid concentrate, 1 mM L-glutamine, 0.1 mM b-mercaptoethanol, and 40 mg/ml N-acetyl cysteine). For the first 2 days, 2 ng/ml of LIF was supplied. After another 7 days of culture in suspension without LIF, neruoepithelial aggregates were dissociated and plated in the same way as for human ESCs.

Tissue Collection

The human fetal tissues used in this study were from patients requesting termination of pregnancy. All the procedures were approved by the institutional review board (Ethics Committee) of Fudan University Shanghai Medical School and the Shanghai Institute of Biological Sciences, Chinese Academy of Science, Shanghai and with the informed consent of the patients. Fetal tissues were obtained within 4 hr after abortion and the developmental stages of fetus specimens were identified according to the anatomy established by Carnegie Institute in Washington, USA. Fetal monkey tissues were obtained from animals at the Wisconsin National Primate Research Center in early pregnancy as previously described (Bondarenko et al., J. Immunol., 2007, 179:8042-8050). The tissues were cut into 15-20 mm frozen sections for immunostaining.

Generation and Analysis of Teratomas

Human ESCs were injected subcutaneously into the backs of severe combined immunodeficient (SCID) mice (Jackson Laboratory) (Xia et al., Stem Cells, 2008, 26:525-533). All animal experiments were performed according to the protocols approved by the Institutional Animal Care and Use Committee, University of Wisconsin.

Statistical Analysis

Data are presented as mean±SEM. Student's tests were used for statistical analysis. P<0.05 was considered significant.

DNA Construction

Pax6 and its mutants were constructed into pLenti vector with a FUGW backbone and an inducible lentiviral vector (Clontech) (Xia et al., Stem Cells, 2008, 26:525-533). Primers for amplifying Pax6a (1-422) and Pax6b (1-436) are as follows: Forward, CATATTCGAGCCCCGTGGAATCC (SEQ ID NO:1); Reverse, TTACTGTAATCTTGGCCAGTATTG (SEQ ID NO:2). Forward primer for amplifying Pax6 ΔPAI (77-422) is ATGAGAGTAGCGACTCCAGAAGTTG (SEQ ID NO:3) and forward primer for Pax6 ΔPD (202-422) is ATGCGACTTCAGCTGAAGCGG (SEQ ID NO:4). For deleting HD in Pax6 (delete 210-269 in Pax6a and 224-283 in Pax6b), two step PCR is used with two additional primers: Forward, CGACTTCAGCTGAAGCGGAAGAAACTGAGGAATCAGAGA (SEQ ID NO:5); Reverse, GTCTTCTCTGATTCCTCAGTTTCTTCCGCTTCAGCTGAAGTCG (SEQ ID NO:6). For subcloning Pax6 dominant negative mutants (D/N), the last 78 amino acids of the PST transactivation domain are removed by the reverse primer, TTGCATAGGCAGGTTATTTGC (SEQ ID NO:7). All the constructs have been verified by DNA sequencing.

Lentivirus Production and Transduction of ESCs

The constructs of lentiviral vectors for knockdown of Pax6 are shown in Figure S2 in Zhang et al., 2010 and lentivirus production was described previously (Xia et al., Stem Cells, 2008, 26:525-533). For transduction of ESCs, human H9 ESCs or mouse ESCs (D3 and 46C) were collected by brief centrifugation. Cell pellets were then incubated with 100 μl of concentrated virus (106 transducing units/ml) at 37° C. for 30 minutes. The virus and cell mixture was then transferred to the MEF feeder layer overnight before changing medium on the next day. Forty-eight hours after infection, blasticidin or puromycin was added to the cells for selecting drug-resistant clones. The final concentration of blasticidin or puromycin was 5 μg/ml for elongation factor-1α (EF1α) promoter and 2 μg/ml for phosphoglycerate kinase (PGK) promoter. To make stable transduced monoclonal lines, ESCs were pretreated with ROCK inhibitor and then trypsinized to single cells before plating on the MEF feeder (Watanabe et al., Nat. Biotechnol., 2007, 25:681-686).

The inducible lentivirus system, purchased from Clontech (Mountain View, Calif.), was modified by replacing the CMV promoter driving rtTA-Advanced in the pLVX-Tet-On Advanced vector with the EF1α promoter to optimize transgene expression in human ESCs.

Western Blotting

Cell pellets were lysed in a lysis buffer (1% Nonidet P-40, 50 mM Tris-HCl, pH 8.0, 0.5% sodium deoxycholate, 150 mM NaCl, 5 mM EDTA, with 10 mM NaF, 10 mM disodium pyrophosphate, and 1× protease inhibitor cocktail, Sigma) and passed through a 281/2 gauge needle several times. The particulate fraction was removed by centrifugation, and 30 μg of proteins in the supernatant were boiled in SDS-PAGE sample buffer and separated by SDS-PAGE.

Microarray Analysis

Luc RNAi and Pax6 RNAi human ESC lines were differentiated to NE cells for 6 days. Total RNA was extracted using Trizol (Invitrogen) and mRNA pooled from two individual lines of each group was hybridized on Affymetrix GeneChip Human Genome HG-U133 Plus 2.0 arrays according to the manufacturer's instructions. The data were deposited in the ArrayExpress database (accession number E-MEXP-2668).

mRNA Extraction and RT-PCR

Total RNA was isolated using the Trizol kit (Invitrogen). 1 μg of total RNA from each sample was reverse transcribed into cDNA and subjected to real-time PCR using the Power SYBR Green kit (Applied Biosystems, UK). Primer oligonucleotides used for real-time PCR were shown in Table 2 (most primers target both human and mouse genes except when they are specifically labeled):

TABLE 2 Gene Forward primer Reverse primer Pax6 TCTTTGCTTGGGAAATCCG CTGCCCGTTCAACATCCTTAG (SEQ ID NO: 8) (SEQ ID NO: 9) Oct4 (human) ACATCAAAGCTCTGCAGAAAGAACT CTGAATACCTTCCCAAATAGAACCC (SEQ ID NO: 10) (SEQ ID NO: 11) Oct4 (mouse) ACATGAAAGCCCTGCAGAAGGAGCT GAGAACGCCCAGGGTGAGCC (SEQ ID NO: 12) (SEQ ID NO: 13) Nanog ATTCTTCCACCAGTCCCAAA ATCTGCTGGAGGCTGAGGTA (SEQ ID NO: 14) (SEQ ID NO: 15) Sox2 GCCCTGCAGTACAACTCCAT TGGAGTGGGAGGAAGAGGTA (SEQ ID NO: 16) (SEQ ID NO: 17) Fabp7 TGTGACCAAACCAACGGTAAT CTTTGCCATCCCATTTCTGTA (SEQ ID NO: 18) (SEQ ID NO: 19) Lhx2 TTACGGCAGGAAAACACGG TGCCAGGCACAGAAGTTAAG (SEQ ID NO: 20) (SEQ ID NO: 21) Six3 ACTACCAGGAGGCCGAGAAG CAGTTCGCGTTTCTTGCTG (SEQ ID NO: 22) (SEQ ID NO: 23) Six6 AACAAGAATGAGTCGGTGCT CAGCGGGAACTTCTTCCTTA (SEQ ID NO: 24) (SEQ ID NO: 25) Map2 GGTCACAGGGCACCTATTCA TGTTCACCTTTCAGGACTGC (SEQ ID NO: 26) (SEQ ID NO: 27) Lmo3 AAGGCACTGGACAAATACTGG CACGCATCACCATCTCAAAG (SEQ ID NO: 28) (SEQ ID NO: 29) Lix1 GGAATTTTGGGAAAGCAAGC CAGCACTGAAAGTTGCCAAA (SEQ ID NO: 30) (SEQ ID NO: 31) Dlk1 TCCTGAAGGTGTCCATGAAAG GTGGTTGTAGCGCAGGTTG (SEQ ID NO: 32) (SEQ ID NO: 33) Meis2 CCAGGGGACTACGTTTCTCA TAACATTGTGGGGCTCTGTG (SEQ ID NO: 34) (SEQ ID NO: 35) Dach1 GGTGGTGTGCAATGTGGA ATGCGGCATGATGTGAGAG (SEQ ID NO: 36) (SEQ ID NO: 37) N-Cad TCCTGATATATGCCCAAGACAA TGACCCAGTCTCTCTTCTGC (SEQ ID NO: 38) (SEQ ID NO: 39) Sox1 GTTTTTTGTAGTTGTTACCGC GCATTTACAAGAAATAATAC (SEQ ID NO: 40) (SEQ ID NO: 41) Nedd9 CCCATCCAGATACCAAAAGG TCTCTCCCACTGGAACTGAA (SEQ ID NO: 42) (SEQ ID NO: 43) Nr2f2 AAGCACTACGGCCAGTTCAC GTCTCATGCCCACTTTGAGG (SEQ ID NO: 44) (SEQ ID NO: 45) Fezf2 CGGCGAGAAGCAGTACAAAT GTTTGCGCACATGTTTCTTT (SEQ ID NO: 46) (SEQ ID NO: 47) Zic1 AGCCACGATGCTCCTGGACGC TGGCCCAGGGCCGCAGCAGC (SEQ ID NO: 48) (SEQ ID NO: 49) Meis1 GATGATTCAAGCCATACAAG GGGGTTCCTCCTGAACGAGT (SEQ ID NO: 50) (SEQ ID NO: 51) Mash1 AACGAGCGCGAGCGCAACCG TTGGAGTAGTTGGGGGAGATG (SEQ ID NO: 52) (SEQ ID NO: 53) Pax3 GCTGTGCCCAGGATGATGC CTGGTACCTGCACAGGATCT (SEQ ID NO: 54) (SEQ ID NO: 55) Lmo1 ACGGAGCGCCCGAGATGATG GGCACAGGATGAGGTTGGCC (SEQ ID NO: 56) (SEQ ID NO: 57) Pou3f2 CCGCAGCGTCTAACCACTAC GTGGGACAGCGCGGTGATCC (SEQ ID NO: 58) (SEQ ID NO: 59) Crx (human) TATTCTGTCAACGCCTTGGCCCTA TGCATTTAGCCCTCCGGTTCTTGA (SEQ ID NO: 60) (SEQ ID NO: 61) RPE65 GCCCTCCTGCACAAGTTTGACTTT AGTTGGTCTCTGTGCAAGCGTAGT (human) (SEQ ID NO: 62) (SEQ ID NO: 63) Chx10 ATTCAACGAAGCCCACTACCCAGA ATCCTTGGCTGACTTGAGGATGGA (human) (SEQ ID NO: 64) (SEQ ID NO: 65) FoxG1 AGAAGAACGGCAAGTACGAGA TGTTGAGGGACAGATTGTGGC (human) (SEQ ID NO: 66) (SEQ ID NO: 67) En1 (human) GGACAATGACGTTGAAACGCAGCA AAGGTCGTAAGCGGTTTGGCTAGA (SEQ ID NO: 68) (SEQ ID NO: 69) Hoxb4 AAAGAGCCCGTCGTCTACC GTGTAGGCGGTCCGAGAG (SEQ ID NO: 70) (SEQ ID NO: 71) Nkx2.1 AACCAAGCGCATCCAATCTCAAGG TGTGCCCAGAGTGAAGTTTGGTCT (human) (SEQ ID NO: 72) (SEQ ID NO: 73) Cdx2 TGGAGCTGGAGAAGGAGTTT CTGCTGCTGCTGTTGCTG (SEQ ID NO: 74) (SEQ ID NO: 75) Gata6 GTGAACTGCGGCTCCATC GTGTGACAGTTGGCACAGGA (SEQ ID NO: 76) (SEQ ID NO: 77) K18 ATGCGCCAGTCTGTGGAG CCTGAGATTTGGGGGCATC (SEQ ID NO: 78) (SEQ ID NO: 79) Lama3 TGTTAATCGGGCAACACAAA GGTGCTTTCCAAAGTTCCTG (SEQ ID NO: 80) (SEQ ID NO: 81) Brachyury  ACAGCCAGCAACCTGGGTA CATGCAGGTGAGTTGTCAGAA (human) (SEQ ID NO: 82) (SEQ ID NO: 83) Sox17 ATACGCCAGTGACGACCAG GCGGCCGGTACTTGTAGTT (SEQ ID NO: 84) (SEQ ID NO: 85) Hnf1b AGAGGGAGGTGGTCGATGTC AGCTGATCCTGACTGCTTTTG (SEQ ID NO: 86) (SEQ ID NO: 87) Pdx1 CAAAGCTCACGCGTGGAAAG TGATGTGTCTCTCGGTCAAG (SEQ ID NO: 88) (SEQ ID NO: 89) Vegfr2 TAGAAGGTGCCCAGGAAAAG CAAGTAGCCTGTCTTCAGTTC (SEQ ID NO: 90) (SEQ ID NO: 91) Gapdh GAAGGTGAAGGTCGGAGTC GAAGATGGTGATGGGATTTC (SEQ ID NO: 92) (SEQ ID NO: 93) For separating Pax6a and Pax6b, primer sets spanning exon5a (Forward: CGGAGTGAATCAGCTCGGTG (SEQ ID NO:94); Reverse: CCGCTTATACTGGGCTATTTTGC (SEQ ID NO:95) were used for regular PCR and analyzed by 2.5% gel.

Chromatin Immunoprecipitation (ChIP)

Inducible GFP, Pax6a-GFP and Pax6b-GFP human ESC lines were treated with 2 μg/ml doxycycline for 1 or 3 days to induce transgene expression. After cross-linking with 1% formaldehyde at 37° C. for 10 min, the cells were harvested by scraping. The fixed cells were then washed and prepared with the EZ-ChIP™ kit according to the manufacturer's suggestions (Millipore). The chromatin was sheared by sonication and incubated with GFP antibody (Chemicon, rabbit IgG). The immunoprecipitates were then washed five times, crosslinks were reversed and immunoprecipitated DNA was subjected to qRT-PCR analysis. Primer pairs against promoter regions of the pluripotent and NE genes were shown in Table 4:

TABLE 4 Targets Forward primier Reverse primer Oct4 ACCAGGCCCCATAATCTACC TTCCCCCACTCTTATGTTGC (SEQ ID NO: 96) (SEQ ID NO: 97) Nanog GGGGGATACTCGGGATACTC GGAAAAGCAGGGTGACATTC (SEQ ID NO: 98) (SEQ ID NO: 99) Fabp7 CGGACATACTTCTGACTTTTTGG GATGCTCTGTGGCAAGATGA (SEQ ID NO: 100) (SEQ ID NO: 101) Six3 ACGGCTGTCTCTGGCTAAGT GGGAAACCTAACGTGACTGG (SEQ ID NO: 102) (SEQ ID NO: 103) Lmo3 CCAGCGAGGGGTAACAGAT CAGCCAATGCACTGAGAAGA (SEQ ID NO: 104) (SEQ ID NO: 105) Meis2 GCCAAACTGAGGCTCTTCAA CCCCCTTTCCTGGTAGGTAT (SEQ ID NO: 106) (SEQ ID NO: 107) Dach1 GTGGAAAACACCCCTCAGAA CTTGTTCCACATTGCACACC (SEQ ID NO: 108) (SEQ ID NO: 109) N-Cad AAAAGCCTAGCCAGCAACAG GCTTTTCTGCTTTGGGTGAC (SEQ ID NO: 110) (SEQ ID NO: 111)

Immunostaining

Antibodies used in this study for immunostaining were Pax6 (1:5,000, mouse IgG, Developmental Studies Hybridoma Bank), Sox1 (1:1,000, goat IgG, R&D), Otx2 (1:2,000, goat IgG, R&D), FoxG1(1:1,500; gift from Dr. Y. Sasai), Sox2 (1:1,000, goat IgG, R&D), Fabp7 (1:1,000, rabbit IgG, Chemicon), N-cadherin (1:1,000, mouse IgG, Santa Cruz Biotechnology), Brachyury (1:50, goat IgG, R&D), AFP (1:500, rabbit IgG, NeoMarkers) and Gata6 (1:500, rabbit IgG, Santa Cruz Biotechnology).

Proliferation Analysis

Proliferation of Pax6 knockdown lines or Pax6 overexpression lines was assessed using a “Click-iT EdU” kit purchased from Invitrogen according to the manufacturer's instructions (Weick et al., Stem Cells, 2009, 27:2906-2916). For Luc RNAi and Pax6 RNAi lines, cells were differentiated for 8 days and 10 μM EdU was added to the cells and allowed for 6 hours of incorporation before fixation and EdU detection. For inducible overexpression lines, cells were treated with doxycycline for 1, 2 and 3 days. The cells were then labeled with EdU for another 6 hours in the presence of doxycycline.

Cell Cycle Analysis

Cells were trypsinized into single cells and fixed in 75% ethanol/PBS overnight. Cells were then washed with PBS and stained with propidium iodide solution (3.8 mM sodium citrate, 50 μg/ml propidium iodide, 0.5 μg/ml RNase A) for 3 hours before analyzed by flow cytometry. 

1. A primate primitive neural stem cell (primate pNSC) wherein the cell overexpresses Pax6.
 2. A population of the primate pNSCs of claim 1, wherein the cells overexpress Pax6.
 3. The population of primate pNSCs in claim 2, wherein the cells continue to proliferate without differentiating.
 4. The population of primate pNSCs in claim 3, wherein the cells continue to proliferate without differentiating for at least a week.
 5. The population of primate pNSCs in claim 3, wherein the cells continue to proliferate without differentiating for at least two weeks.
 6. The population of claim 2, wherein the cells are human pNSCs.
 7. A method of creating a population of primate pNSCs from primate embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) comprising the step of: overexpressing Pax6 within a population of ESCs or iPSCs, wherein the expression level of Pax6 is sufficient to suppress the expression of Sox1 and Oct4.
 8. The method of claim 7, wherein the overexpression of Pax6 is via an inducible system.
 9. The method of claim 7, wherein the overexpression of Pax6 is via a lentiviral vector.
 10. The method of claim 7, wherein the overexpression of Pax6 is under the control of elongation factor 1α promoter in the lentiviral vector.
 11. The method of claim 7, wherein the overexpression of Pax6 is via adding recombinant and/or exogenous Pax6 protein to the cells directly.
 12. The method of claim 9, wherein the lentiviral vector is an inducible lentiviral vector.
 13. The method of claim 7, wherein the primate is human.
 14. A method of creating a population of primate regional neural stem cells comprising the steps of: (a) overexpressing Pax6 within a population of primate ESCs or iPSCs wherein the expression level of Pax6 is sufficient to suppress the expression of Sox1 and Oct4; and (b) suppressing Pax6 expression and differentiating the cells of step (b) into regional neural stem cells.
 15. The method of claim 14 wherein the regional neural stem cells are selected from the group consisting of forebrain cells, midbrain cells and spinal cells.
 16. The method of claim 14 wherein the primate is human.
 17. A method of creating a population of primate pNSCs from primate regional neural stem cells comprising the step of: overexpressing Pax6 within a population of primate regional neural stem or progenitor cells wherein the expression level of Pax6 is sufficient to reprogram the cells to the primate pNSC stage.
 18. The method of claim 17 wherein the primate is human.
 19. A method of treating a patient with brain tumor or overgrowth of cell transplants by suppressing Pax6 expression comprising the steps of inhibiting Pax6 expression in the tumor cells or the overgrown cell transplants.
 20. The method of claim 19, wherein the suppression of Pax6 expression is through Pax6 RNAi, block of Pax6 transcription or acceleration of Pax6 degradation. 